Proteins and Wave Functions

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Friday, March 30, 2018

This is an attempt to explain MCTS to myself. If I made any mistakes let me know in the comments.

Let's say we have to make three sets of binary decisions (e.g. left/right). This leads to $2^3$ = 8 possible outcomes (A-H) and let's say three of these (A, E, and F) are desirable (i.e. "winners"). We'd like to find one or more of these, without having to go through all the options, which can be represented by a tree-graph as shown here (the circles as called nodes and the lines are called edges).

We start at the top of the tree and pick one path on each side of the tree at random, basically by flipping a coin at each node to decide wether we go left or right (hence Monte Carlo). Let's say we end up at point A and G.

We now go to the second layer of the graph and on each node record whether we found a winner ($w_i$ = 1) or not ($w_j$ = -1) and the number of times we visited the node ($n_i = n_j$ = 1). In the top node we add the wins and losses (1 + -1 = 0) and the total number of attempts ($N$ = 2).

Now we compute the "action" ($a_i$) for each edge in the first branch point according to
$$ a_i = \frac{w_i}{n_i}+c \sqrt{\frac{\ln (N)}{n_i}}$$
$c$ is the exploration parameter that, theoretically, is $\sqrt{2}$ but in practise is an empirical parameter. Here I'll use $c$ = 4.

Now we start at the top node and choose the node with the highest action, which in this case it the left one. From this node we choose a direction at random and repeat this process until we hit the end of the tree. Let's say we ended up at C. C is not a winner so we update the $w_i$s and $n_i$s on this path and add $w_i$ and $n_i$ to the first node we chose at random.

Now we update the actions. Note that because $N$ changes, the action on the right hand side of the tree also changes. In fact, that action is now larger than on the left, so in our fourth exploration we'll now start exploring the right side of the tree further.

We now repeat this process as many times as we can afford. The path with the most action at the end of the simulation is chosen as the best one.

You'll notice that paths A and B will never be explored again because we (arbitrarily) chose to branch to the right at some point. So another option that's often used, is to chose random paths leading in both directions as we did in the very first step.

Tuesday, March 6, 2018

We submitted this paper to ACS Omega January 31st and the reviews just came back

Reviewer: 1

Recommendation: Publish after minor revisions.

Comments:
The authors explored the CBH approach proposed by Sengupta and Raghavachari to compute the reaction enthalpy of a series of organic reactions using semi-empirical and low-cost HF/DFT as the low-level method. They also discussed the origin of errors for several cases that exhibited very large errors. The results will be very useful to the computational chemistry community, in terms of identifying effective means to compute reaction energetics and better ways to improve low-cost methods.

I have only a few minor comments:
1. It appears that dispersion correction was not included for DFTB3 and some NDDO methods. For reactions that involve very large molecules, dispersion may make a non-negligible contribution, as found, for example, for Diels-Alder reactions in the recent benchmark analysis by Gruden et al. (J. Comp. Chem. 38, 2171-2185).

2. There are several typos: line 55 of pg 2, "corrections WERE not included"; line 48 of pg 6, there is one additional "is".

3. It might be useful to report and comment on the computational cost for the different approaches. For example, PBEh-3c is still rather expensive compared to the semi-empirical methods.

4. Is there a "simple" explanation for the difference between xTB and DFTB3? For example, does the improved description of frequencies by xTB make a major difference?

Reviewer: 2

Recommendation: Publish after minor revisions.

Comments:
The authors have carried out an analysis of the performance of highly efficient computational methods for the computation of enthalpies of organic reactions using the connectivity-based hierarchy. The methods considered include DFT, HF, and a range of semi-empirical methods. The analysis is clear and some of the reported findings are indeed significant. While the good performance of DFT and HF is consistent with previous results, the lack of significant improvement with semi-empirical methods is particularly noteworthy. The paper is acceptable for publication after the authors address the following comment.

A more detailed analysis is reported for reaction 19 that is an outlier for some methods such as HF. In this system, the larger errors are attributed partly to the presence of the strained oxirane ring. Similarly, reaction 23 poses problems for some semi-empirical methods due to the presence of larger errors involving allene. In light of these observations, it may be useful to add a cautionary note to the range of problems that can be studied with such methods. I suggest a small paragraph to address the potential limitations of the inexpensive methods for such systems containing unusual bonding situations.

Sunday, March 4, 2018

First of all I have fixed a bug in the bond order energy function so the program now suggests significantly fewer structures. Second I have written some code that creates input files for a QM program (GFN-xTB) and analyses the output. I choose GFN-xTB because it's a super fast semiempirical QM method that is also reasonably accurate. I have tried to keep things fairly modular so that it's easy to interface it with other QM programs (more details in the code comments).

Using the Diels-Alder reaction as an example, staring with ethene and butadiene as the reactant the program now suggests 28 other structures with energies no more than 100 kcal/mol higher than the reactants. I choose 100 kcal/mol because the energy function is very crude.

All structures are then optimized with GFN-xTB and I now select structures with energies no more than 20 kcal/mol higher than the reactants. I choose a lower value here because I trust the energy function a bit more. I use the electronic energy plus an estimate of the translational entropy, but the code can easily be modified to use free energies. This narrows it down to 21 structures (ranked by energy below) in addition to the reactants, so the bond order energy function is actually doing quite well.

You'll notice that some of the structures appears to have two H atoms, but this is in fact an H2 molecule. The reason for this is that the code that translates the Cartesian coordinates back to SMILES uses a distance criterion to assign bonds and that apparently needs some tweaking for H2. It's important to recompute the SMILES because the bonds can rearrange during the geometry optimization.

I also need to fix the code for calculations on atoms where GFN-xTB doesn't print out coordinates.

The next step is to find TSs connecting all these structures to the reactants to find the lowest barrier.

Saturday, March 3, 2018

I want to use Google Colaboratory for my python course, but the module we use for animation doesn't work there because the necessary libraries are not installed. I had planned to spend part of the weekend to see if I could find a solution but by amazing coincidence a tweet in my Twitter stream this morning had the answer!

The answer is simply to display the images sequentially and clear the output each time with clear_output(wait=True) from IPython.display. You can see the demo code I wrote below. This works very nicely on my off-line notebook (where you want to execute this line in a cell above the notebook itself: %matplotlib inline) while the animation is a bit choppy on Colaboratory, presumably due to network latency. But it's certainly good enough.

Saturday, February 17, 2018

Here's a simple script for generating rotamers. It assumes the input geometry is reasonable and perturbs the dihedral angles of $n$ rotateable bonds by $\pm 120^\circ$. It makes all $3^n$ combinations of dihedral angles but if that is larger than a user-defined cutoff it will pick a random subset. Rotateable bonds include alcohol, phenols, and primary amines, but also amide bonds. It doesn't know about equivalent atoms, so it will happily rotate a tert-butyl or trifluoromethyl group.

Wednesday, February 14, 2018

This is a follow up to this post, but now we (that is Mads) use up to 1000 structures. To summarise: we use RDKit to generate $n$ starting conformations of neutral ("0") and protonated ("+") acebutolol and minimise them in aqueous solution using PM3/COSMO (MOPAC) and PM3/SMD /GAMESS) for a maximum of 200 steps.

The plot shows the lowest energy structure relative to the lowest energy found among all values of $n$. For example, the lowest PM3/COSMO value for the neutral form is found when generating 400 starting geometries and using 1000 starting structure, the lowest energy found is 1.1 kcal/mol higher.

I was a bit worried about the numerical stability of the COSMO and SMD methods, i.e. that the $n$ = 400 structure was generated in the $n$ = 1000 run, but had a higher energy for some reason. The figure above shows the lowest energy structure found ($n$ = 400) in purple and the structure most closely resembling it in the $n$ = 1000 search in green. So the $n$ = 400 structure was not generated in the $n$ = 1000 run.

Acebutolol has 12 rotateable bonds and roughly $3^{12}$ = 500,000 possible rotamers and RDKit samples these randomly. So, on hindsight, it is not surprising that $n$ = 400 and $n$ = 1000 randomly chosen samples do not both contain the lowest energy structure.

Incredibly (at least to me), the green structure is 1.7 kcal/mol higher in energy than the green. But, further optimisation of the green structure does not change energy, nor does changing the optimiser to EF instead of the default. I even rotated the molecule and restarted to the optimisation to test the robustness of the COSMO grid. But, no, this energy difference due to what I think is a minor strutural difference appears to be real. This means that the conformational PES is quite rugged, i.e. small structural changes can result in relatively big energy changes.

As it stands, pKa-predictions using PM3/COMSO or SMD (where I use $n$ > 100) will have a ca 1 pKa unit random error due to the conformational search and increasing $n$ is not really going to decrease that very much.

I'm not sure what to do about that. We might try combining several low-$n$ conformational searches, with different random seeds. Alternatively, we may have to implement some sort of directed search, e.g. a genetic algorithm but that is going to be quite expensive for an SQM based method.

Alternatively, we have to pick the structures we use based on an MM screen where we can do a more thorough search but then we really need a MM/continuum solvation method interface. If you have other ideas I'd be happy to hear about it.

Let me end with a challenge. Can you make a robust method that can find a PM3/COSMO energy equal to or lower than -183.01 kcal/mol for neutral acebutolol? And that is converged with respect to starting geometry and number of conformers tested? The MOPAC keywords are

Zimmerman defines an elementary reaction step as a chemical rearrangement "with no more than two connections breaking and two connections forming simultaneously, while maintaining the upper and lower limits for coordination number of each atom." Two structures that are related in this way are very likely to be connected by a single transition state.

The code generates all such states for a given molecule and then selects the "best ones" based on a crude energy function based on bond dissociation energies. The idea is then to optimize the molecules using a QM method to refine the selection and then locate the TS connecting the selected structures to the input structures. The atom ordering should be preserved (haven't checked yet) so they are suitable for interpolation-based methods such as NEB or GSM.

The default is to lists all structures with energies no higher than 200 kJ/mol compared to the input structure and to use homolytic bond cleavage, i.e. a C-H bonds is broken into a C and H radical, rather than, say, C- and H+, but this can be controlled by the "heterolytic" keyword.

Using the heterolytic option will result in incorrectly charged fragments in some cases, but these should be weeded out by the energy criterion. For example, if you input acetylene the code will generate HC3- + HC3- instead of HC3- + HC3+, but I didn't feel like writing complicated code to fix this since these possibilities will no be presented to the user because they are too high in energy.

The figure at the bottom shows the results using 1,3-butadiene + ethene as input. For some reason, RDKit has trouble displaying H2 molecules so they have been removed and acetylene looks very weird (e.g. for comp64). There are 88 structures in all, but that number could be reduced significantly be removing molecules with unsaturated atoms and/or three- and four-membered rings.

In his paper, Zimmerman shows 5 selected structures obtained using his implementation:

The first three also appear below as comp8, comp21, and comp54, while the last two are seemingly missing. However, they actually don't correspond to elementary steps since more than 2 bonds are broken or formed, but result from the subsequent QM optimization of comp7 and comp52 where additional bonds are formed between unsaturated C atoms.